[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,868] [INFO] DQC Reference Directory: /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,535] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,535] [INFO] Running command: cat /var/lib/cwl/stg9ea6821d-c097-41af-a459-8ce2ef51d90f/OceanDNA-b22846.fa | prodigal -d OceanDNA-b22846/cds.fna -a OceanDNA-b22846/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:48:08,439] [INFO] Task succeeded: Prodigal
[2023-03-16 03:48:08,440] [INFO] Task started: HMMsearch
[2023-03-16 03:48:08,440] [INFO] Running command: hmmsearch --tblout OceanDNA-b22846/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/reference_markers.hmm OceanDNA-b22846/protein.faa > /dev/null
[2023-03-16 03:48:08,757] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:48:08,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ea6821d-c097-41af-a459-8ce2ef51d90f/OceanDNA-b22846.fa]
[2023-03-16 03:48:08,802] [INFO] Query marker FASTA was written to OceanDNA-b22846/markers.fasta
[2023-03-16 03:48:08,803] [INFO] Task started: Blastn
[2023-03-16 03:48:08,803] [INFO] Running command: blastn -query OceanDNA-b22846/markers.fasta -db /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/reference_markers.fasta -out OceanDNA-b22846/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:09,478] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:09,479] [INFO] Selected 33 target genomes.
[2023-03-16 03:48:09,479] [INFO] Target genome list was writen to OceanDNA-b22846/target_genomes.txt
[2023-03-16 03:48:09,496] [INFO] Task started: fastANI
[2023-03-16 03:48:09,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea6821d-c097-41af-a459-8ce2ef51d90f/OceanDNA-b22846.fa --refList OceanDNA-b22846/target_genomes.txt --output OceanDNA-b22846/fastani_result.tsv --threads 1
[2023-03-16 03:48:38,499] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:38,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:38,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:38,504] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:38,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:38,504] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.6217	67	1852	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.4171	57	1852	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.4002	65	1852	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:38,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22846/tc_result.tsv
[2023-03-16 03:48:38,504] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:38,504] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:38,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/checkm_data
[2023-03-16 03:48:38,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:38,639] [INFO] Task started: CheckM
[2023-03-16 03:48:38,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22846/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22846/checkm_input OceanDNA-b22846/checkm_result
[2023-03-16 03:50:00,797] [INFO] Task succeeded: CheckM
[2023-03-16 03:50:00,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:50:00,802] [INFO] ===== Completeness check finished =====
[2023-03-16 03:50:00,802] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:50:00,802] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22846/markers.fasta)
[2023-03-16 03:50:00,803] [INFO] Task started: Blastn
[2023-03-16 03:50:00,803] [INFO] Running command: blastn -query OceanDNA-b22846/markers.fasta -db /var/lib/cwl/stga7c78f2c-340b-4f56-b7c1-2361a7ce1dfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22846/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:50:01,758] [INFO] Task succeeded: Blastn
[2023-03-16 03:50:01,759] [INFO] Selected 22 target genomes.
[2023-03-16 03:50:01,759] [INFO] Target genome list was writen to OceanDNA-b22846/target_genomes_gtdb.txt
[2023-03-16 03:50:01,873] [INFO] Task started: fastANI
[2023-03-16 03:50:01,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea6821d-c097-41af-a459-8ce2ef51d90f/OceanDNA-b22846.fa --refList OceanDNA-b22846/target_genomes_gtdb.txt --output OceanDNA-b22846/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:50:26,051] [INFO] Task succeeded: fastANI
[2023-03-16 03:50:26,056] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:50:26,057] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_016779365.1	s__JABMPE01 sp016779365	79.8601	516	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	78.5944	744	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	76.3214	193	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238335.1	s__Fuerstia sp014238335	76.0552	54	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.6217	67	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.0352	53	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.0316	52	1852	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:50:26,057] [INFO] GTDB search result was written to OceanDNA-b22846/result_gtdb.tsv
[2023-03-16 03:50:26,057] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:50:26,058] [INFO] DFAST_QC result json was written to OceanDNA-b22846/dqc_result.json
[2023-03-16 03:50:26,058] [INFO] DFAST_QC completed!
[2023-03-16 03:50:26,058] [INFO] Total running time: 0h2m53s